Displaying all 9 publications

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  1. Lee XW, Mat-Isa MN, Mohd-Elias NA, Aizat-Juhari MA, Goh HH, Dear PH, et al.
    PLoS One, 2016;11(12):e0167958.
    PMID: 27977777 DOI: 10.1371/journal.pone.0167958
    Rafflesia is a biologically enigmatic species that is very rare in occurrence and possesses an extraordinary morphology. This parasitic plant produces a gigantic flower up to one metre in diameter with no leaves, stem or roots. However, little is known about the floral biology of this species especially at the molecular level. In an effort to address this issue, we have generated and characterised the transcriptome of the Rafflesia cantleyi flower, and performed a comparison with the transcriptome of its floral bud to predict genes that are expressed and regulated during flower development. Approximately 40 million sequencing reads were generated and assembled de novo into 18,053 transcripts with an average length of 641 bp. Of these, more than 79% of the transcripts had significant matches to annotated sequences in the public protein database. A total of 11,756 and 7,891 transcripts were assigned to Gene Ontology categories and clusters of orthologous groups respectively. In addition, 6,019 transcripts could be mapped to 129 pathways in Kyoto Encyclopaedia of Genes and Genomes Pathway database. Digital abundance analysis identified 52 transcripts with very high expression in the flower transcriptome of R. cantleyi. Subsequently, analysis of differential expression between developing flower and the floral bud revealed a set of 105 transcripts with potential role in flower development. Our work presents a deep transcriptome resource analysis for the developing flower of R. cantleyi. Genes potentially involved in the growth and development of the R. cantleyi flower were identified and provide insights into biological processes that occur during flower development.
    Matched MeSH terms: Angiosperms/genetics*
  2. Cai L, Arnold BJ, Xi Z, Khost DE, Patel N, Hartmann CB, et al.
    Curr Biol, 2021 03 08;31(5):1002-1011.e9.
    PMID: 33485466 DOI: 10.1016/j.cub.2020.12.045
    Despite more than 2,000-fold variation in genome size, key features of genome architecture are largely conserved across angiosperms. Parasitic plants have elucidated the many ways in which genomes can be modified, yet we still lack comprehensive genome data for species that represent the most extreme form of parasitism. Here, we present the highly modified genome of the iconic endophytic parasite Sapria himalayana Griff. (Rafflesiaceae), which lacks a typical plant body. First, 44% of the genes conserved in eurosids are lost in Sapria, dwarfing previously reported levels of gene loss in vascular plants. These losses demonstrate remarkable functional convergence with other parasitic plants, suggesting a common genetic roadmap underlying the evolution of plant parasitism. Second, we identified extreme disparity in intron size among retained genes. This includes a category of genes with introns longer than any so far observed in angiosperms, nearing 100 kb in some cases, and a second category of genes with exceptionally short or absent introns. Finally, at least 1.2% of the Sapria genome, including both genic and intergenic content, is inferred to be derived from host-to-parasite horizontal gene transfers (HGTs) and includes genes potentially adaptive for parasitism. Focused phylogenomic reconstruction of HGTs reveals a hidden history of former host-parasite associations involving close relatives of Sapria's modern hosts in the grapevine family. Our findings offer a unique perspective into how deeply angiosperm genomes can be altered to fit an extreme form of plant parasitism and demonstrate the value of HGTs as DNA fossils to investigate extinct symbioses.
    Matched MeSH terms: Angiosperms/genetics*
  3. Daud N, Taha RM, Hasbullah NA
    Pak J Biol Sci, 2008 May 01;11(9):1240-5.
    PMID: 18819532
    Efficient plant regeneration of Saintpaulia ionantha (African violet) has been obtained in the present study. MS medium supplemented with 1.0 mg L(-1) IAA and 2.0 mg L(-1) Zeatin resulted in 100% shoot regeneration and induced the highest number of shoots (average 15.0 +/- 0.8 shoots per explant) after being cultured for 8 weeks. The above hormone combination was optimum for shoot regeneration. Most of Saintpaulia ionantha plantlets derived from tissue culture system could be hardened and transferred to the greenhouse conditions with 84.0 +/- 1.6% success rate. However, regenerated plantlets of Saintpaulia ionantha (even after 12-months-old) failed to flower. Morphological characters of regenerated plantlets of Saintpaulia ionantha were observed and compared with in vivo (intact) plants. Regenerated plantlets showed some differences in morphological characters, such as height and leaf size, texture and colour, but the plantlets showed no variation in leaf arrangement and leaf margin. However, the morphological characters of the regenerated plantlets were found to be unstable.
    Matched MeSH terms: Angiosperms/genetics*
  4. Wee SL, Tan SB, Jürgens A
    Phytochemistry, 2018 Sep;153:120-128.
    PMID: 29906658 DOI: 10.1016/j.phytochem.2018.06.005
    The plants of the enigmatic genus Rafflesia are well known for their gigantic flowers and their floral features such as pungent floral scent and vivid dark color, which mimics the food/brood sites of carrion. However, information on the pollination biology of this plant group remains limited and mostly anecdotal. In the present paper, we studied the floral volatiles of R. cantleyi Solms-Laubach and their role in pollinator attraction. To achieve these aims, the floral scent was collected in situ in the field using a dynamic headspace method followed by chemical analysis via GC-MS. The olfactory preferences of pollinators to the identified chemical compounds, were tested singly and in blends, in flight tunnel bioassays and compared with responses to headspace floral extracts. In addition, flower-visiting calliphorid flies and the local carrion fly community were sampled and identified. Five species of calliphorid flies (subfamilies of Chrysomyinae and Calliphorinae), all females, were found on the flowers, whereas nine species were found in the traps that were baited with tainted meat in the surrounding habitat. However, only flower visitors of one blow fly species, Chrysomya chani Kurahashi, were observed to carry R. cantleyi pollen after visiting male flowers. The floral volatiles emitted by male flowers in full bloom were dominated by two sulphur-containing compounds, dimethyl disulfide (DMDS) and dimethyl trisulfide (DMTS). These were accompanied by other minor compounds such as benzenoids (4), monoterpenoids (4), trace amounts of aliphatic compounds (1), and sesquiterpenes (1). In flight-tunnel bioassays, a female-specific positive response of C. chani flies to individual DMDS, DMTS, and a blend of DMDS and DMTS was evident. Our findings suggest that R. cantleyi biochemically mimics carrion and that relative ratio of oligosulfides in the floral scent play a key role in sex-biased pollinator specialization, attracting only female C. chani carrion flies to the flowers.
    Matched MeSH terms: Angiosperms/genetics
  5. Redwan RM, Saidin A, Kumar SV
    BMC Plant Biol, 2015;15:196.
    PMID: 26264372 DOI: 10.1186/s12870-015-0587-1
    Pineapple (Ananas comosus var. comosus) is known as the king of fruits for its crown and is the third most important tropical fruit after banana and citrus. The plant, which is indigenous to South America, is the most important species in the Bromeliaceae family and is largely traded for fresh fruit consumption. Here, we report the complete chloroplast sequence of the MD-2 pineapple that was sequenced using the PacBio sequencing technology.
    Matched MeSH terms: Angiosperms/genetics
  6. Chiang TY, Chiang YC, Chen YJ, Chou CH, Havanond S, Hong TN, et al.
    Mol Ecol, 2001 Nov;10(11):2697-710.
    PMID: 11883883
    Vivipary with precocious seedlings in mangrove plants was thought to be a hindrance to long-range dispersal. To examine the extent of seedling dispersal across oceans, we investigated the phylogeny and genetic structure among East Asiatic populations of Kandelia candel based on organelle DNAs. In total, three, 28 and seven haplotypes of the chloroplast DNA (cpDNA) atpB-rbcL spacer, cpDNA trnL-trnF spacer, and mitochondrial DNA (mtDNA) internal transcribed spacer (ITS) were identified, respectively, from 202 individuals. Three data sets suggested consistent phylogenies recovering two differentiated lineages corresponding to geographical regions, i.e. northern South-China-Sea + East-China-Sea region and southern South-China-Sea region (Sarawak). Phylogenetically, the Sarawak population was closely related to the Ranong population of western Peninsula Malaysia instead of other South-China-Sea populations, indicating its possible origin from the Indian Ocean Rim. No geographical subdivision was detected within the northern geographical region. An analysis of molecular variance (AMOVA) revealed low levels of genetic differentiation between and within mainland and island populations (phiCT = 0.015, phiSC = 0.037), indicating conspicuous long-distance seedling dispersal across oceans. Significant linkage disequilibrium excluded the possibility of recurrent homoplasious mutations as the major force causing phylogenetic discrepancy between mtDNA and the trnL-trnF spacer within the northern region. Instead, relative ages of alleles contributed to non-random chlorotype-mitotype associations and tree inconsistency. Widespread distribution and random associations (chi2 = 0.822, P = 0.189) of eight hypothetical ancestral cytotypes indicated the panmixis of populations of the northern geographical region as a whole. In contrast, rare and recently evolved alleles were restricted to marginal populations, revealing some preferential directional migration.
    Matched MeSH terms: Angiosperms/genetics*
  7. Rose JP, Kleist TJ, Löfstrand SD, Drew BT, Schönenberger J, Sytsma KJ
    Mol Phylogenet Evol, 2018 05;122:59-79.
    PMID: 29410353 DOI: 10.1016/j.ympev.2018.01.014
    Inferring interfamilial relationships within the eudicot order Ericales has remained one of the more recalcitrant problems in angiosperm phylogenetics, likely due to a rapid, ancient radiation. As a result, no comprehensive time-calibrated tree or biogeographical analysis of the order has been published. Here, we elucidate phylogenetic relationships within the order and then conduct time-dependent biogeographical and diversification analyses by using a taxon and locus-rich supermatrix approach on one-third of the extant species diversity calibrated with 23 macrofossils and two secondary calibration points. Our results corroborate previous studies and also suggest several new but poorly supported relationships. Newly suggested relationships are: (1) holoparasitic Mitrastemonaceae is sister to Lecythidaceae, (2) the clade formed by Mitrastemonaceae + Lecythidaceae is sister to Ericales excluding balsaminoids, (3) Theaceae is sister to the styracoids + sarracenioids + ericoids, and (4) subfamilial relationships with Ericaceae suggest that Arbutoideae is sister to Monotropoideae and Pyroloideae is sister to all subfamilies excluding Arbutoideae, Enkianthoideae, and Monotropoideae. Our results indicate Ericales began to diversify 110 Mya, within Indo-Malaysia and the Neotropics, with exchange between the two areas and expansion out of Indo-Malaysia becoming an important area in shaping the extant diversity of many families. Rapid cladogenesis occurred along the backbone of the order between 104 and 106 Mya. Jump dispersal is important within the order in the last 30 My, but vicariance is the most important cladogenetic driver of disjunctions at deeper levels of the phylogeny. We detect between 69 and 81 shifts in speciation rate throughout the order, the vast majority of which occurred within the last 30 My. We propose that range shifting may be responsible for older shifts in speciation rate, but more recent shifts may be better explained by morphological innovation.
    Matched MeSH terms: Angiosperms/genetics
  8. Song AA, Abdullah JO, Abdullah MP, Shafee N, Rahim RA
    Int J Mol Sci, 2012;13(2):1582-97.
    PMID: 22408409 DOI: 10.3390/ijms13021582
    Vanda Mimi Palmer (VMP), an orchid hybrid of Vanda tesselata and Vanda Tan Chay Yan is a highly scented tropical orchid which blooms all year round. Previous studies revealed that VMP produces a variety of isoprenoid volatiles during daylight. Isoprenoids are well known to contribute significantly to the scent of most fragrant plants. They are a large group of secondary metabolites which may possess valuable characteristics such as flavor, fragrance and toxicity and are produced via two pathways, the mevalonate (MVA) pathway or/and the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway. In this study, a sesquiterpene synthase gene denoted VMPSTS, previously isolated from a floral cDNA library of VMP was cloned and expressed in Lactococcus lactis to characterize the functionality of the protein. L. lactis, a food grade bacterium which utilizes the mevalonate pathway for isoprenoid production was found to be a suitable host for the characterization of plant terpene synthases. Through recombinant expression of VMPSTS, it was revealed that VMPSTS produced multiple sesquiterpenes and germacrene D dominates its profile.
    Matched MeSH terms: Angiosperms/genetics*
  9. Ng SM, Lee XW, Mat-Isa MN, Aizat-Juhari MA, Adam JH, Mohamed R, et al.
    Sci Rep, 2018 11 22;8(1):17258.
    PMID: 30467394 DOI: 10.1038/s41598-018-35173-1
    Parasitic plants are known to discard photosynthesis thus leading to the deletion or loss of the plastid genes. Despite plastid genome reduction in non-photosynthetic plants, some nucleus-encoded proteins are transported back to the plastid to carry out specific functions. In this work, we study such proteins in Rafflesia cantleyi, a member of the holoparasitic genus well-known for producing the largest single flower in the world. Our analyses of three transcriptome datasets, two holoparasites (R. cantleyi and Phelipanche aegyptiaca) and one photosynthetic plant (Arabidopsis thaliana), suggest that holoparasites, such as R. cantleyi, retain some common plastid associated processes such as biosynthesis of amino acids and lipids, but are missing photosynthesis components that can be extensions of these pathways. The reconstruction of two selected biosynthetic pathways involving plastids correlates the trend of plastid retention to pathway complexity - transcriptome evidence for R. cantleyi suggests alternate mechanisms in regulating the plastidial heme and terpenoid backbone biosynthesis pathways. The evolution to holoparasitism from autotrophy trends towards devolving the plastid genes to the nuclear genome despite the functional sites remaining in the plastid, or maintaining non-photosynthetic processes in the plastid, before the eventual loss of the plastid and any site dependent functions.
    Matched MeSH terms: Angiosperms/genetics
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